› 6pss

Electron Microscopy
3.5Å resolution

Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1.5a) with TraR and mutant rpsT P2 promoter

Released:
DOI: 10.2210/pdb6pss/pdb
PDB entry 6pss coloured by chain, front view.
PDB entry 6pss coloured by chain, side view.
PDB entry 6pss coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Stepwise Promoter Melting by Bacterial RNA Polymerase.
Chen J, Chiu C, Gopalkrishnan S, Chen AY, Olinares PDB, Saecker RM, Winkelman JT, Maloney MF, Chait BT, Ross W, Gourse RL, Campbell EA, Darst SA
Mol Cell 78 275-288.e6 (2020)
PMID: 32160514
Related structures: EMD-20462

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-120458 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
DNA-directed RNA polymerase subunit alpha Chains: G, H, M
Molecule details ›
Chains: G, H, M
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: I
Molecule details ›
Chain: I
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A8V2 (Residues: 1-1342; Coverage: 100%)
Gene names: JW3950, b3987, groN, nitB, rif, ron, rpoB, stl, stv, tabD
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chain: J
Molecule details ›
Chain: J
Length: 1430 amino acids
Theoretical weight: 158.07 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A8T7 (Residues: 2-1407; Coverage: 100%)
Gene names: JW3951, b3988, rpoC, tabB
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: K
Molecule details ›
Chain: K
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor RpoD Chain: L
Molecule details ›
Chain: L
Length: 616 amino acids
Theoretical weight: 70.72 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
Protein TraR Chain: N
Molecule details ›
Chain: N
Length: 72 amino acids
Theoretical weight: 8.19 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P41065 (Residues: 2-73; Coverage: 99%)
Gene names: ECOK12F083, traR
Sequence domains: Prokaryotic dksA/traR C4-type zinc finger
DNA (85-MER) Chain: O
Molecule details ›
Chain: O
Length: 85 nucleotides
Theoretical weight: 26.24 KDa
DNA (85-MER) Chain: P
Molecule details ›
Chain: P
Length: 85 nucleotides
Theoretical weight: 26.19 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-20462
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

Approaches to Heterogeneity in Native Mass Spectrometry.
Rolland et al. (2022)
5 more

3 mentions without citation

Diverse and unified mechanisms of transcription initiation in bacteria.
Chen et al. (2021)
2 more